6S0J

Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JLQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29315% PEG3350, 0.16 M sodium citrate and 9% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.0941.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.943α = 90
b = 69.604β = 94.4
c = 57.751γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.569.699.70.0440.0540.0310.99810.12.966685
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.53990.9881.2110.6910.4191.22.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2JLQ1.557.6563340328599.540.14720.1450.1888RANDOM26.885
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.466
r_dihedral_angle_4_deg16.323
r_dihedral_angle_3_deg12.391
r_dihedral_angle_1_deg6.73
r_rigid_bond_restr2.248
r_angle_refined_deg1.586
r_angle_other_deg1.451
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.466
r_dihedral_angle_4_deg16.323
r_dihedral_angle_3_deg12.391
r_dihedral_angle_1_deg6.73
r_rigid_bond_restr2.248
r_angle_refined_deg1.586
r_angle_other_deg1.451
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3372
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction